GROMACS version: 2020.1-Ubuntu-2020.1-1
GROMACS modification: No
I am a new GROMACS user with a background in Mechanical Engineering, so I am new to MD in general. I have completed some tutorials and am beginning to work through my own trials.
I am looking to investigate the dielectric properties of different concentrations of dimethyl sulfoxide in water. I acquired my DMS files from the PDB website and converted to .gro using acpype, with hopes to run trials using GAFF.
I attempted to follow the steps listed here: https://bioinformaticsreview.com/20210204/tutorial-md-simulation-with-mixed-solvents-using-gromacs/
With some small adjustments for my own purposes.
I have been stuck on the energy minimization step, I am currently encountering a fatal error:
ERROR 1 [file tip3p.itp, line 7]:
Atomtype OW not found
This occurs when I run
gmx grompp -f em.mdp -c DMS_solv.gro -p DMS_GMX.top
I don’t understand why it is not recognizing the atomtype 0W, as it is present in the solvent and the file included in topology.
where em.mdp is
; to test
; echo 0 | gmx editconf -f DMS.pdb.mol2_GMX.gro -bt octahedron -d 1 -c -princ
; gmx grompp -f em.mdp -c out.gro -p DMS.pdb.mol2_GMX.top -o em.tpr -v
; gmx mdrun -ntmpi 1 -v -deffnm em
; Parameters describing what to do, when to stop and what to save
integrator = steep ; Algorithm (steep = steepest descent minimization)
nsteps = 500 ; Maximum number of (minimization) steps to perform
nstxout = 10
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbour list and long range forces
cutoff-scheme = Verlet
rlist = 1.2 ; Cut-off for making neighbour list (short range forces)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.2 ; long range electrostatic cut-off
vdw-type = cutoff
vdw-modifier = force-switch
rvdw-switch = 1.0
rvdw = 1.2 ; long range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions
DispCorr = no
; vmd em.gro em.trr
DMS_gmx.top is
; DMS.pdb.mol2_GMX.top created by acpype (v: 2022.7.21) on Wed Apr 17 02:07:10 2024
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333333333
; Include DMS_GMX.itp topology
#include "DMS_GMX.itp"
#include "amber94.ff/tip3p.itp"
; Ligand position restraints
#ifdef POSRES_LIG
#include "posre_DMS.pdb.mol2.itp"
#endif
[ system ]
DMS.pdb.mol2 in water
[ molecules ]
; Compound nmols
DMS.pdb.mol2 80SOL 161
tip3p 161
DMS_solv.gro is a ~1:2 molal solution of 80 molecules DMS and 141 molecules of water. I can attach the full file if necessary but a few lines including info for DMS and water are shown below:
80UNL S 791 1.415 1.632 2.468
80UNL O 792 1.462 1.768 2.507
80UNL C 793 1.238 1.623 2.505
80UNL C1 794 1.396 1.630 2.288
80UNL H 795 1.186 1.708 2.460
80UNL H1 796 1.198 1.530 2.467
80UNL H2 797 1.225 1.627 2.613
80UNL H3 798 1.496 1.638 2.243
80UNL H4 799 1.351 1.536 2.257
80UNL H5 800 1.335 1.715 2.256
81SOL OW 801 0.225 0.275 0.996
81SOL HW1 802 0.260 0.258 1.088
81SOL HW2 803 0.137 0.230 0.984
82SOL OW 804 0.569 1.275 1.165
82SOL HW1 805 0.476 1.268 1.128
82SOL HW2 806 0.580 1.364 1.209
I apologize if anything is glaringly incorrect, my goal with this process has been to find a procedure and nail down correct values for parameters for cutoff radius etc, later.
Please let me know if there’s any more necessary information to help me figure out this issue, thank you!